May 3, 2010
PubPDF: Easily Download PDFs for Articles Found in PubMed!
Many of you have eagerly embraced PubGet (Illinois.pubget.com) as a way to easily view and obtain PDFs from your PubMed searches (see Biotechnology Information Center News, October 2009). Here’s another option: PubPDF. (Currently only available for PCs; not Macs.)
PubPDF, from Quosa, will enable you to immediately view and download PDFs for articles you’ve located via a standard search of PubMed. Once the PubPDF plugin is installed to work with your browser (Firefox or IE) you will immediately see on the PubMed search results screen an Acrobat (PDF) icon in front of all the titles of articles to which we have access! You can click on the icon to view the article. Or, you can select multiple articles (click on the box in front of the citation) and download the PDFs using a file-naming structure that you choose (e.g., author name – date – journal abbreviation).
Watch the Video
First, watch the short video ,”Introducing PubPDF”: http://quosa.com/quosa-labs
Install the PubPDF Plugin
Firefox Users:
Go to: http://pubpdf.com
You will see a message advising you to download the Coral IE Tab. Click on the link and select “Add to Firefox.” Follow the instructions to install. You will need to restart Firefox to complete the installation of Corel IE Tab. When you restart Firefox, you will get this message: “Please turn on "Coral IE Tab". To do this in Firefox: Click on Tools / Addons / Coral IE Tab / Options. Under the Sites Filter tab add the site http://pubpdf.com/ and Click Add.
IE Users:
Go to: http://pubpdf.com
You will need to allow a small Active X add-on to install. The add-on is QB Plus ActiveX Component, from Quosa, Inc. You may receive a security warning or window, but you must allow this add-on for PubPDF.
Customize PubPDF for Use at the U of Illinois
To use PubPDF in conjunction with PubMed, you will now use http://pubpdf.com as your PubMed URL. You will notice that most of the window looks like the standard PubMed window; but there is also a small toolbar above the PubMed window:
In the PubPDF toolbar:
** Click on the dropdown arrow to the right of the box that says Pubmed, and choose Set PubMed Home Page. Enter this for your homepage: http://tinyurl.com/28yurj9. This tells PubPDF to use the U of I library definition for PubMed. You’ll want to specify that you want to use the U of I PubMed URL so you retain the option to obtain articles through our “Discover” links when PubPDF doesn’t locate the PDF of an article for you. (If you prefer, instead of the tinyurl you can type in this longer URL: http://www.library.uiuc.edu/proxy/go.php?url=http://www.ncbi.nlm.nih.gov/pubmed?otool=uiuclib&holding=uiuclib,f1000,deepblue)
** Click on the ellipsis (…) (to the left of the folder icon) to specify the folder into which you wish to have downloaded PDFs saved and to specify the naming convention you wish to use for the downloaded PDFs (e.g. First Author_Publication Year _ Journal Abbreviation).
Using PubPDF
To use PubMed with PubPDF, start at http://pubpdf.com/.
Run your search. Notice the Adobe PDF icons that appear in front of most citations! Click on an icon to view the PDF.
To download PDFs: Select citations and click on the Sigma (∑).
To download citations to EndNote: Select PubMed citations and click on “Export”.
If you need an article that does not have the Adobe icon in front of the citation, click through to the PubMed abstract view of the citation; you will find the familiar U of I Discover button that will help you locate the article you need.
Note: Use the PubPDF “back” and “forward” buttons to navigate…not your browser’s back / forward buttons.
Tip: Scopus, a multidisciplinary database that covers both the sciences and social sciences, also has an option to download and name PDFs (up to 50 at a time)! No additional plugins are necessary to use the download feature in Scopus.
Questions? Contact Katie Newman, Biotechnology Librarian, 2130 IGB, florador@illinois.edu, 217-265-5386.
Posted by florador at 10:58 AM
February 23, 2010
Tips for Making your Life Easier!
PaperPlane
If you use PubGet and Firefox is your preferred browser, be sure to install Pubget’s PaperPlane. Then after searching PubMed in your usual fashion, you can click on the PaperPlane toolbar icon and be shunted to PubGet, where you can immediately start reading the full text of papers that match your PubMed search criteria! (Of course, you can also just use Pubget to search PubMed.)
To get PaperPlane, just drag it to your Firefox bookmarks toolbar from this website:
http://pubget.com/site/help/paper_plane
EndNote Addins
If you’re an EndNote user, you’ll want to add the capacity to more readily view the full text of articles. Please visit the U of Illinois EndNote Support site for instructions on customizing your EndNote program:
http://www.library.illinois.edu/biotech/endnotesupport.html.
Follow the instructions for “Setting Up EndNote to Work with Discover”.
After making the customizations:
If you are using EndNote 8 or higher, you’ll be able link out to the full text of the article. Just right-click on the citation in Endnote, and click on the link to “OpenURL”. This feature is similar to what happens when you click on the “Discover” link in PubMed, Web of Science, etc. You will be shunted to the publisher’s site for the full text of the article.
If you are using EndNote X3, you will, in addition, be able to pull over (download) PDF files for the articles in your EndNote library for which the University Library holds subscriptions. You can do this one by one, or for many articles at once. The PDFs will be stored on your computer; automatically links to the stored PDFs will be added to the EndNote record for the article. You don’t need to worry about naming the file, etc. This feature was available to a limited extent in version X2, as well.
Handy Free Web Tools
ZamZar (www.zamzar.com): Convert from PDF to Word documents. (Other file conversions also available.)
PrintWhatYouLike (www.printwhatyoulike.com/) Tired of printing web pages only to find your printout is full of ads, empty space and other junk you don't want? PrintWhatYouLike is a free online editor that lets you format any web page for printing in seconds! Great for editing out unwanted columns in web tables, too. Tip: Install the Bookmarklet so you can simply click on it when you get to a page you want to edit and print.
Awesome Highlighter (www.awesomehighlighter.com/) Lets you highlight text on a page and creates a URL for the page with your highlight, which you can share with others. E.g., here’s my homepage, with a few highlights: http://awurl.com/SLqxzbHNe. Tip: Add the Firefox Add-on so you can just click on the link when you land on a page that you want to highlight!
TinyURL (www.tinyurl.com) Converts LONG URLs to tiny URLs – great for sending URLs in emails or for posting URLs to web sites!
Posted by florador at 1:30 PM
Need a Biological Protocol?
Did you realize that the University Library subscribes to quite a few “protocols” sources? Find links to these resources at http://www.library.illinois.edu/biotech/researchtools/
Wiley’s Current Protocols
Updated quarterly and searchable, you have e-access to such popular titles as:
Current Protocols in Molecular Biology
Current Protocols in Immunology
Current Protocols in Bioinformatics
Current Protocols in Cell Biology
as well as CPs in Cytometry, Human Genetics, Magnetic Resonance Imaging, Microbiology, Neuroscience, Nucleic Acid Chemistry, Pharmacology, Protein Science, and Toxicology.
Nature Protocols
Includes peer-reviewed protocols published in Nature Protocols, as well as protocols derived from Nature research journals and from content posted directly to the site by the research community. All protocols are searchable and may be commented upon.
Cold Spring Harbor Protocols
Cold Spring Harbor Protocols is an interdisciplinary monthly journal providing a source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. The searchable site includes protocols from the Cold Spring Harbor courses (Xenopus, Mouse, Proteomics, Yeast Genetics); protocols from “Emerging Model Organisms: a Laboratory Manual”; and kit protocols from Abcam, Bethyl, Bio-Rad, Epicentre, and Qiagen. Part of the site is devoted to recipes for reagents, including purchasing information.
Methods in Enzymology
Volume 1 (1955) to present available electronically. This venerable series covers enzymology in the broadest possible sense, covering topics such as photosynthesis, nucleic acids, membranes, hormones, vitamins, immunological techniques, interferons, recombinant DNA, plant molecular biology, microbial toxins, mass spectroscopy, ion channels, and much more.
Questions? Comments? Send to Katie Newman, Biotechnology Librarian, 2130 IGB, florador@illinois.edu, 217-265-5386
Posted by florador at 1:25 PM
April 25, 2008
Local Assistance for NIH Grantees
The University of Illinois Library stands ready to assist local NIH grantees meet the requirements of the recently inaugurated NIH Public Access Policy.
We've created the NIH Public Access Mandate website that offers step-by-step help through the process and will help you decide if you have the RIGHT to deposit your manuscripts into the PubMed Central system.
Here you will find:
- General Information and answers to frequently asked questions about the Policy.
- Resources to help you figure out if you have the RIGHT to deposit your work in PubMed Central
- Basic, step by step instructions for depositing your work.
- How you can have the Library do the submission for you.
- Useful Links & Local Contacts who can help you
Please let us know if we can be of assistance!
Katie Newman
Biotechnology Librarian and Scholarly Communication Officer
florador@uiuc.edu
217-265-5386
Sarah Shreeves
IDEALS Coordinator
sshreeve@uiuc.edu
217-244-3877
Posted by florador at 1:31 PM
November 15, 2007
Firefox Plugin for PubMed Users at the U of Illinois
If you're a bio researcher who uses the Firefox browser and PubMed, you'll want to read this!
Leslie McNeil, the NCSA researcher who manages the National Microbial Pathogen Data Resource (NMPDR), has created a Firefox plugin for U of I researchers who frequently search PubMed!
About Firefox Plugins:
Are you used to searching Google by typing in queries in the top right-hand side of the Firefox toolbar? Did you know that you can add additional search options so you can choose to search Wikipedia, Google Scholar, the U of I domain, or many other search sites, instead? All you need to do is add additional FireFox plugins.
You'll find many additional Firefox plugins from the following sources:
https://addons.mozilla.org/en-US/firefox/browse/type:4
http://mycroft.mozdev.org/
http://www.searchplugins.net/pluginlist.aspx
To load them into Firefox, all you have to do is click on the plugin's name.
Among my favorite plugins (available from the Mycroft site) are:
Wikipedia / Univ. of Illinois / Google Scholar / Google Books / Google News / Google Images / Amazon / Ebay / Flickr / Yahoo / Epicurious / IMDB / YouTube / ...
About the Firefox PubMed plugin for U of I Researchers:
Leslie McNeil has created a customized a PubMed FireFox plugin for the U of Illinois researchers. Install it from this site:
http://mycroft.mozdev.org/download.html?name=PubMed+U+of+I+full+text&sherlock=yes&opensearch=yes&submitform=Search
To install the plugin, just click on the link for the name of the plugin.
To use it, just click on the Firefox drop down indicator next to the box where you normally would type in a Google search. Choose to search PubMed instead of Google and type in your PubMed search. You'll be brought to the PubMed site with all the usual University of Illinois subscriptions and options** intact -- that is, you'll see which articles we have direct e-access to, and you'll see the UI Discover button that lets you discover other options for obtaining the articles.
Give it a try! I think you'll agree it's handy!
**That is, you'll go to the same PubMed search as if you started with this URL:
http://www.library.uiuc.edu/orr/get.php?instid=406312
Posted by florador at 4:39 PM
September 18, 2007
Illinois Biotechnology Organization Formed
The Illinois Biotechnology Organization (IBO) was recently formed by several graduate students and post-docs for the purpose of "gathering together students, post-doc, professors etc. that are involved in the biotechnology area at the University of Illinois in Champaign-Urbana."
At the IBO website one will find gathered together University links of significance to biotechnology as well as a page of links that point to information about biotechnology.
The IBO is planning its first event, a social hour, for Monday, October 29th from 7-9 PM. It will be held in Room 210 of the Illini Union. All are welcome to attend, but it is requested that you register by October 22nd by sending an email to:uiuc.ibo@gmail.com.
The IBO social hour is being held in conjunction with the 2007 Biotechnology Job Fair, which is being held on Tuesday, October 30th, from 9-12 and 1-3:30, in the Illini Union. Deadline for registration for the Job Fair is October 1st.
Posted by florador at 11:14 AM
August 1, 2007
BioText: Search for Text within the Captions of Journal Articles
Below is a posting from the BioMed Central blog announcing that the BioText search engine is available! Many of you will recall that several months ago it's developer, Marti Hearst gave a presentation at UI, to the Bioinformatics Group, about Biotext.
BioText, in it's current rendition allows one to perform text searches within the captions of figures (as well as the abstracts) in ~150 journals housed in BioMed Central.
Here's a link to the search engine:
http://biosearch.berkeley.edu/
Here's a listing of the journals you'll be searching (includes BMC Bioinformatics!) (click on the "Collection" tab): "The current collection consists of more than 150 journals, 20,000 articles, and 80,000 figures."
http://biosearch.berkeley.edu/index.php?action=about
Research report (Bioinformatics):
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm301v1
http://bioinformatics.oxfordjournals.org/cgi/reprint/btm301v1.pdf
Some searching tips...
If you search for several words, it does an OR search. That is, it's not like Google, which does an AND search!
To force it to search on several words in a Google-like mode, put a "+" in front of the word, or enclose a phrase in quotations. To search for word stems, put an asterisk after the word stem.
Examples of legitimate searches would be....
(Searching over "captions (list view)", with number of "hits"...)
bee 30
"honey bee" 5
bee bees 44
"Apis mellifera" 35
microarray genom* 4973
+microarray +genom* 107
+microarra* +genom* 128
Enjoy!
Katie
=====================
As seen on the Open Access blog, an excerpt from the BioMed Central Blog:
=====================
Matt Hodgkinson, BioText - a search engine for open access figures, BioMed Central blog, July 31, 2007. Excerpt:
At the ISMB conference we met Anna Divoli, a postdoc at the University of California, Berkeley, who showed us the BioText Search Engine, which she was presenting as a poster, and has recently published....
I came across it briefly earlier this month thanks to the blog of medical librarian David Rothman, who described it as "A supercool way to search PubMed Central", which is a pretty good description!
It is part of the text mining BioText project and goes beyond the abstract searching in MEDLINE seen previously to extend searching to the figure legends of Open Access journals in PubMed Central.
As the homepage of PubMed Central notes, "All the articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access". Because Open Access explicitly allows the reuse of the content of the articles in these journals (which include all 170+ BioMed Central journals) this has allowed the BioText people to create a search engine that allows keyword searching of abstracts, figure legends, titles and authors, returning results sorted by date and relevance, and in two formats: abstracts with figure thumbnails and legends, or figure legends with thumbnails....
Anna hinted at upcoming functions such as returning snippets that match the search terms from the full text of the article (much as Google Scholar does). We look forward to these further developments, and we'd like to thank Anna, Marti Hearst and the others on the BioText team for developing such a useful and user friendly tool. This is a great example of how Open Access allows others to make further use of published work, in ways that the authors or publishers had not anticipated.http://blogs.openaccesscentral.com/blogs/bmcblog/
Posted by florador at 1:49 PM
July 12, 2007
Learn of New Literature Based on Its Taxa
If you're interested in keeping track of the literature for a particular species, read on to learn about a new service, uBioRSS, that harvests info from hundreds of publisher table of contents alerts!
If you set up searches using this service based on any level of taxa for any type of organism, you'll receive email alerts as new articles are published.
--------------
Matthew Cockerill, Track the latest open access research relating to your favorite taxon, BioMed Central blog, June 26, 2007. Excerpt:
uBioRSS is a nifty service from the MBLWHOI Library at Woods Hole, which harvests bibliographic information about new articles from publishers' RSS feeds, and then passes them through the uBio taxonomic classification system which identifies any species that are mentioned in the article, and classifies the article appropriately.
This makes it possible to browse the literature taxonomically, so that, for example you might view a list of all the latest articles on cetaceans far more easily than can be done using plain text search.
What's more, it is possible to filter articles by source, so you an easily taxonomically browse just BioMed Central's open access articles. The site also offers an alerting service, so you can choose to be notified of new articles which relate to your particular taxon of interest.
uBioRSS is a great example of the way in which semantic enrichment can add value to the literature, and shows how it is particularly effective when combined with open access, as this then allows the semantic enrichment to be applied not just to the text of the title and abstract, but to the entire full text. To see an example of this in action, check out the UBio taxonomically-enhanced PubMed Central full text search....
Comment:
I tested this out to see if it had built-in feeds for the Honeybee, Apis mellifera, and it did! Click Here.
It pulled articles published during the last month in such journals as:
Florida Entomologist
Journal of Medical Entomology
BMC Genomics
Southeastern Naturalist
Australian Journal of Entomology
Science
BMC Developmental Biology
New South Wales Department of Primary Industries
PLOS Biology
The Southwestern Naturalist
Journal of Mammalogy
Insect Molecular Biology
Physiological Entomology
So, you might want to sign up for this service from uBioRSS as an adjunct to the alerting emails that you are already receiving (I Hope!) from Web of Science, PubMed, Biological Abstracts, Scopus, Faculty of 1000, CAB Abstracts, and so on!
Please let me know if you'd like some help setting up alerts in your field!
Posted by florador at 11:32 AM
July 10, 2007
Provost's Letter in Support of Retaining Publishing Rights
From Provost Linda Katehi, in an email sent to the U of Illinois Faculty, 7/10/07
==========
Dear Colleague,
New opportunities created by electronic publishing and archiving are changing the business of scholarly publication. Because traditional publication agreements transfer copyrights to publishers and restrict electronic distribution by the author and their institution, publishers appear to have captured much of the benefit of these changes.
In November 2006, faculty governance leaders from CIC universities discussed these issues that affect scholarly communication and called for a concrete strategy that would help faculty retain more control over their published intellectual property. Subsequently, the CIC provosts issued a
Statement on Publishing Agreements and an Addendum to Publication Agreements for CIC Authors. (http://www.cic.uiuc.edu/programs/CenterForLibraryInitiatives/Archive/Report/CICAuthRtsFINAL16May07.pdf) The Addendum is intended to be used by faculty entering into publication agreements with journal publishers or presses. It supports authors rights to use their own published work in teaching and research, to post a publication on a personal website, or to deposit it in a repository maintained by their institution or a professional association. IDEALS (www.ideals.uiuc.edu) is the University of Illinois institutional repository.
Late this Spring, the U of I Senate endorsed the principles expressed in the CIC Provosts Statement and Addendum; encouraged faculty to consider using it as well as other publication agreement addenda that increase their rights in reproducing, distributing, and archiving their own work; and asked the CIC Provosts to provide leadership in negotiating with publishers to develop new publication agreements that provide CIC authors and institutions greater rights for use, distribution and archiving their published scholarly works.
It is our responsibility as scholars to ensure that our work is available as widely as possible to maximize its scholarly impact, accessibility, and educational use. I encourage you to use the Addendum and to deposit your research and scholarship in IDEALS, which provides reliable and persistent access to its holdings.
===============
You may read more about what the U of I is doing at the Scholarly Communication website. See:
What the U of I is doing
What YOU can do.
Posted by florador at 9:46 AM
July 9, 2007
PLoS Hires ScienceBlogs Blogger to Encourage Interactivity
With thanks to Becky Smith for the heads up...
Bora Zivkovic, chief blogger at ScienceBlog's "A Blog Around the Clock", has been hired by the Public Library of Science to encourage readers to comment on the papers that are published by the various PLOS journals.
Each PLOS article provides a link whereby readers may "provide a response" to the article. Browsing through several issues of PLOS Biology indicates to me that so far this option has been underutilized so it appears Bora will have a big task ahead of himself.
It seems to me that such comments on articles could certainly add extra value to the original piece -- they could elaborate on related experiments, refute the findings, or comment on the significance of the article much as Faculty of 1000 Biology recommendations do.
Good luck, Bora!
Posted by florador at 11:24 AM
June 5, 2007
Broad Impact: Refreshing Your Statistics Knowledge
Have you discovered Faculty of 1000 Biology, yet? It's a great tool for discovering hidden gems and important papers in particular areas. I like to think of it as a really good student advisory committee that selects, recommends, and critiques the top "must read" articles in all areas of Biology!
Here's a news blurb from BioMed Central, the publisher of F1000:
Five Faculty of 1000 Biology members have recently singled out an Exceptional Broad Impact paper that is of high relevance to researchers in all fields of Biology, as it provides guidance to biologists for navigating the often tricky world of data representation -- in particular the use of error bars."This paper should be read by anyone who is trying to present experimental data graphically." comments David Stephens (University of Bristol, UK), Faculty of 1000 Biology member for Cell Biology.
Andy Groves (House Ear Institute, USA), a Faculty of 1000 Biology member for Developmental Biology goes on to say "This wonderful article clearly explains how experimental variation is measured and displayed, and describes how different kinds of error bars can mean very different things. This paper is a must read for every scientist who thinks that triplicate plates from a single experiment counts as n=3 !!!!!"
"Personally, I have filed the pdf in a safe place, and I plan to consult it every time I send a graph for publication." concludes Etienne Joly (CNRS, France), a Faculty of 1000 Biology Member for Immunology.
The Faculty of 1000 Biology structure makes it possible to identify papers of broad interest, irrespective of the journal in which they are published. Go to the Faculty of 1000 Biology website to see the full comments of all the evaluating Faculty Members on this Exceptional Broad Impact paper.
Posted by florador at 10:21 AM
May 21, 2007
Link to Full-text Articles from EndNote
Are you an EndNote user? If so, you'll be interested in learning how you can set up EndNote so it communicates with our OpenURL resolver to provide you with links to the full-text of journal articles!
You may have seen the Discover link 
in PubMed, Web of Science, and many other article databases. When you click on the Discover link in these databases a new browser window pops up that provides links to the full text of the article (if we have an e-subscription), and several other facets about the article [read more about Discover].
You may enable this same technology in EndNote by following the instructions provided on the page, Linking to Full-text Journal Articles from EndNote Using Discover.
Posted by florador at 4:27 PM
January 25, 2007
Publish Videos of Your Experiments Online - for Free
The Journal of Visualized Experiments (2006-) is truly living up to the old adage that a picture is worth a thousand words. This online, open access journal is
publishing visualized (video-based) biological research studies. This publication aims to solve some of the most difficult problems in the contemporary life science research:
- low transparency and reproducibility of biological experiments
- time-consuming learning of experimental techniques
Each video-article will include step-by-step instructions on an experiment, a demonstration of equipment and reagents, and a short discussion by experts describing possible technical problems and modifications. Every scientist planning on a biological experiment will be able to access the database, find videos relevant to their work, and use them as protocols. High effectiveness of visualized instructions, as compared to currently used written protocols, will decrease failure rates for biological experiments, and, thus, facilitate significant savings in time and cost. It will also increase reproducibility of published experiments, one of the main problems in the current life science research.
There is no charge to authors to submit or have their protocols published. Each submission will be reviewed by members of an editorial board, but, at this time, will not be rigorously peer-reviewed (that will come later). The time lapse from the date of submission to the date of publication should be no longer than 7-14 days. At the present time, there are 17 videos available in JoVE.
Of course, researchers have been putting their videos up on their personal websites and in sites such as YouTube. See for yourself: search for microarray in YouTube or in GoogleVideo.
Posted by florador at 10:14 AM
January 4, 2007
Accessing from Off-Campus: PubMed, Journals and other Library Resources
There are two ways to access Library resources from off-campus. For both of these, you will need to know your UIUC NetID and password. Your NetID is usually the username that precedes your @uiuc.edu email address; your password is usually NOT the same as your email password!
Pros and Cons:
Pro |
Con |
|
| Method 1: Use Library-provided URLs to access journals and indexes. |
|
|
| Method 2: Use VPN to provide your off-campus computer with a virtual UIUC IP address. |
|
|
| Recommendation: |
|
|
Method One:
In order to access e-journals and library databases from off-campus, use the links provided from the UIUC Library’s Online Research Resources (ORR) site, http://www.library.uiuc.edu/orr/.
All the resources in the ORR have been registered in a database. When you click on these links from off campus, you’ll be routed through a campus server that will prompt you to provide your NetID and password, thus authenticating yourself as a legitimate UIUC affiliate. Usually you’ll just have to authenticate yourself once per browser session in order to access any library resource.
Example: PubMed
It is particularly important that you use the proper UIUC-specific URL to access PubMed we have created a UIUC-specific PubMed URL that will let you see the e-journals for which UIUC specifically has access. Whether you're on campus or not, this URL will also allow you to see the articles that have been recommended as ‘must reads’ in the Faculty of 1000 database and to see the "Discover" links, which provide you with another avenue for getting to full text and interlibrary loan forms. If you've used the UIUC-PubMed URL from off-campus, you'll be able to click on the links for e-journals that are found within PubMed and gain access to the full text of all the journal articles for which we hold subscriptions.
The standard PubMed URL, which is freely available to the whole wide world, is: http://www.ncbi.nlm.nih.gov/PubMed/
But to be recognized as a UIUC user, and thus to be able to access from within PubMed the UIUC e-journals from off-campus, you should use this URL instead: http://www.library.uiuc.edu/orr/get.php?instid=406312
(You'll find a link for this URL from the Library's ORR page, or from UIUC departmental library homepages such as Biology, Biotechnology Information Center, ACES Funk, and more.)
When you click on the PubMed link from off-campus, you'll be prompted to provide your NetID and password. After you do this, you'll find that you're at the UIUC-specific site for PubMed:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=uiuclib,f1000.
As long as you keep the browser session running, you will remain authenticated as a UIUC affiliate and should be able to click on links for e-journals that are found within PubMed or elsewhere and gain access to the full text of all the journal articles for which we hold subscriptions.
Similarly, if you want to access Biological Abstracts, Web of Science, EmBase, CAB Abstracts, Faculty of 1000, etc., from off-campus: start with the link found in the Library's ORR!
Method Two:
Use CITES' Virtual Private Networking (VPN) to establish a connection to the University, and to authenticate yourself as a UIUC affiliate. When you use VPN to access resources from off-campus, it's as if your computer were physically located on campus! However, in order to use this method, you must be able to install a small program on the computer you are using to access UIUC resources from off-campus. Read more about VPN at http://www.cites.uiuc.edu/vpn/.
Step One:
Download and install the proper VPN program for your computer from CITES.
Step Two:
Download and install the Library profile. (There is just the one library profile file for all computer types.)
Using the VPN program is simple (You'll do this every day):
- Close any browser sessions that may be open on your home computer.
- Start up the VPN program.
- Double-click on Library Profile (you will also see another profile available, "off-campus"; don't use that one!)
- A pop-up screen will appear; login using your NetID and Password.
- Now you may open your browser (Firefox, Netscape, Internet Explorer, etc.)
After you've logged in via VPN, you should be able to go about your business as if you were located on campus as your computer will perform as if it were coming accessing the internet from the UIUC IP range. That is, you can go directly to the publisher's web sites, etc.
Caveat: there are a FEW resources for which the VPN mode of access won't work, usually due to restrictions placed by publishers. In MOST of those cases, you'll be able to get in via the link in the Online Research Resources directory.
Posted by florador at 3:29 PM
February 27, 2006
PubMed has been Discovered!
This morning PubMed was Discovered!
"Discover" is the name of the link the Library has been populating most of our major databases with that allows you to discover whether we have e-access to a journal, a print subscription, or whether you need to request the item via Interlibrary Loan.
Bookmark this URL for PubMed!
IF you use the UIUC-specific link for Pubmed
http://www.library.uiuc.edu/orr/get.php?instid=406312
(which can be found in the Library's ORR (Online Research Resource),
http://www.library.uiuc.edu/orr/ )
you'll now see that ALL the records have Discover links on them!!
Recommendation:
- Use the Library's URL to access PubMed http://www.library.uiuc.edu/orr/get.php?instid=406312
- After you've run your search, choose to "Display" in "Citation" format. This lets you see all the buttons and links at glance.
- And choose to "Show" at least 100 citations at a time.
- If you see the blue link "Full text provided by the UIUC Library", click on it for direct access to the e-version of the article.
- If that link isn't present, then click on the "Discover UIUC Full Text Linking" button. This will cause the Discover window to pop up, and you'll see your options --
- link(s) for the full text
- a link that will search the UIUC Library online catalog, which will inform you if we have a print subscription
- a link to interlibrary loan, so you can request the item from another university; the form will already be filled in for you
- a link to RefWorks, so you can easily import the citation into Refworks
- a link to Google Scholar, so you can look for similar articles
- link(s) for the full text
I ran a search this morning in PubMed for articles about Apis mellifera (the honeybee), and looked at the first 100 records:
- 77 of these had the "Full text provided by the UIUC Library" link, so I could go directly to the full text of the article
- Via the Discover link, I could go directly to 11 more articles. (These were articles that did NOT have the "Full text provided by the UIUC Library" link)
- And via the Discover link I found that we have a print subscription that contains 2 more articles.
- This left just 10 (out of 100) articles that I would have had to request via Interlibrary loan. And Discover helped with this, too, since it filled in the Interlibrary form for me!
Bottomline:
The University Library wants you to get the research articles that you need! In many cases they are now available electronically. But the worst case scenario is that you'll need to request an article via InterLibrary loan.
Learn more about Discover:
http://www.library.uiuc.edu/discover/ or
http://www.library.uiuc.edu/blog/bicnews/archives/2005/12/discover_full_t.html
Posted by florador at 3:06 PM
January 11, 2006
Wikis and Blogs by Scientists - a new way to communicate science
A recent news item in Nature,
- the wiki, OpenNetWare, an effort to share biological engineering protocols
- "A senior US epidemiologist who blogs once or twice a day under the pseudonym 'Revere' on his public-health blog Effect Measure, has attracted a diverse readership. "About 1,500 people visit each day," he says. "If someone told me that I could show up at a lecture hall every day and deliver a short opinion, and that 1,500 people would show up to hear me, I'd be pretty satisfied — 1,500 is twice the subscription of many speciality journals."
- If you want to dip your feet in the waters, and are a computational biologist, you might want to sign on to blog at Nodalpoint.org, a blog for bioinformatics
- Blog.Bioethics.Net, a companion blog to the American Journal of Bioethics
- Cancer Dynamics, "Musings from the coalface in a research lab modelling cancer as a complex system"
UIUC has a subscription to BioMedCentral's Faculty of 1000 database, which is a way to tap into the articles that senior biologists have identified as "key". But what about learning / contributing to the blogosphere, where everybody has an opinion?
Read the full Nature article at: http://www.nature.com/nature/journal/v438/n7068/full/438548a.html
Posted by florador at 5:18 PM
December 2, 2005
"Discover" Full Text for Research Articles!
Starting this week, you will begin to see a new button, the Discover Button, next to all the citations in many of our electronic resources, including index and abstract databases.
WHAT IS THE PRIMARY FUNCTION OF THE DISCOVER BUTTON?
The primary function of the button is to give you a link to the full-text version of the article, if UIUC has rights to it.
While many of the databases already have links to the full text in them (e.g., PubMed, Web of Science), through the Discover button, you should uncover e-access for even more publications! If we don't have e-access to the article, the Discover window will provide you with other tools for obtaining the article.
WHAT DOES THE DISCOVER BUTTON DO?
When you click on the Discover button, a new window will pop up that will contain links to various types of resources:
1] Links to the full text of the article (if UIUC has e-access).
2] A link to the UIUC Online Catalog record for the journal (so you can see if we have print / e-access to the journal)
3] A link to Interlibrary Loan, with the citation information already filled in.
4] A link to RefWorks, which will automatically add the citation to RefWorks ***
5] A link to Google Scholar, so you may search for other articles by this author, or other articles on the topic in the Google Scholar database.
WHERE CAN I FIND THE DISCOVER BUTTON?
We're starting by putting the Discover button in all the citations in the Engineering Village databases (Compendex and Inspec), and the databases and journals that we get access to via the ScienceDirect interface. It's also already available in RefWorks*** and in Google Scholar.
The Discover button will appear in most other indexes and abstracts (e.g., PubMed and Web of Science) before the start of the Spring term, 2006. Stay tuned for announcements!
Learn more about the new Discover service, go to:
http://www.library.uiuc.edu/biotech/discover.htm
***RefWorks:
If you don't know about RefWorks, please go to: http://www.library.uiuc.edu/refworks.
Training is available in December, see:
http://www.library.uiuc.edu/blog/bicnews/archives/2005/12/refworks_traini.html
RefWorks is like a web-based "EndNote"! That is, it's a place where you can build your own database of citations, and then pull these citations out of the database to use in your papers -- automatically formatting the citations in the proper format for whichever journal you're submitting your paper to! And, pertinent to this e-mail, ALL of your citations in RefWorks will have a Discover button, providing you with easy access to the full-text of the article!
Faculty: Get your students, grad and undergrads, using RefWorks! It's available for free (courte$y of the Library and CITES) for everyone on campus to use.
Katie
Posted by florador at 3:21 PM
February 28, 2005
Keeping up with Biotech News
Bioentrepreneur
Life scientists interested in commercializing their research can look to Bioentrepreneur -- a comprehensive Web portal from the Nature Publishing Group -- for "authoritative, independent advice provided by experts and industry insiders." Bioentrepreneur offers current business development news, a resource toolkit, profiles of life sciences companies, and much more. Users must create a free personal account with Bioentrepreneur to access all features of the Web site. Note: You may opt to receive regular email updates concerning new listings on the Bioentrepreneur site.
Genomeweb (sign up for free, daily alerts, too!)
UIUC Carver Biotechnology Center. Sign up to receive announcements from the UIUC Carver Biotechnology Center listserv.
Use PubCrawler to receive email "alerts" as citations of interest are added to PubMed or Genbank.
Surfwax. Aggregated current news on: biotech / genetic engineering / genome projects / molecular biology / other biological topics.
Biotech & drug news from Yahoo: Top Stories or Latest headlines
Topix.net for Biotech industry news
CropBiotech Update. Sign up to receive a weekly emailed update on crop biotechnology issues from ISAAA (International Service for the Acquisition of Agri-biotech Applications SEAsiaCenter). Take a look at the most recent issue. To sign up for the newsletter, send an e-mail message to knowledge.center@isaaa.org leaving the subject blank and entering the one-line text message as follows: SUBSCRIBE Crop Biotech Network.
Posted by at 2:34 PM